The Oncoming Storm
by PondGirl11
Summary: Prequel to The Storm Has Arrived. The Doctor thinks he will never find somebody after the Ponds. He couldn't be more wrong. Set after The Doctor, The Widow and The Wardrobe, however in this AU he leaves after Christmas Dinner and doesn't take them with him.
1. Crash

The Oncoming Storm

AN: Hey guys! This is my first fan fiction, so please don't go hard on me! I know it's a short chapter, but I didn't want to reveal too much at the very beginning.

Disclaimer: I own nothing, not even my own house.

The Doctor was annoyed. He had only been alone for fifteen minutes and already Amy and Rory's absence was evident as he absent-mindedly flicked the controls, not caring where he went. He had left in a puff of smoke, leaving his best friends behind him. He wasn't even in the mood for fish fingers and custard, his usual absolute favourite. He thought about going back to see them, but he didn't want to seem weak; after all, _he _left _them_.

Suddenly, there was an almighty roar as if there was a trapped beast being finally overcome with claustrophobia, and the TARDIS shuddered. The Doctor, now wary, clutched the scanner and peered at the readings. All fours. That was definitely not a good sign. He slowly, in case there was another quake, moved towards the doors. He anxiously looked out, and then stepped out of the TARDIS in confusion.

He knew exactly which planet this was, but apart from that he was completely lost.

AN: If there's anything you want me to include in this story, any hints or characters, please let me know in a PM or a review!


	2. Torchwood Tower

AN: I'd like to dedicate this chapter to fantasticbeasts for being my first follower and reviewer! This chapter will be ever so slightly longer, but still short as I don't want to reveal everything too quickly! Remember, anything or anyone you'd like me to include in the story, just let me know!

_He anxiously looked out, and then stepped out of the TARDIS in confusion._

_He knew exactly which planet this was, but apart from that he was completely lost._

Earth. What was he doing on Earth? Of all the planets to accidentally land on, why _Earth?_ Gazing around again, something tugged at his memory, and he squinted into the sun, trying to make sense of his déjà vu. First came confusion (he hadn't been here before had he?), then recognition (of _course_). Canary Wharf. Where he lost Rose.

He felt a long concealed sob rising in his throat, but then checked himself, and remembered something. He ran back into the TARDIS and checked the scanner. The fours had been replaced by nines, which was definitely better. The screen shifted to show the date, and location, confirming his whereabouts and surprising him with the date. It was 2006, but _before_ he came here with Rose. He frowned at his beloved machine. 'Why have you brought me here?' he murmured.

Walking back outside, he realised that it must still be Torchwood tower. Spontaneously deciding to pay them a visit, he strolled in and stopped at the sight of Yvonne Hartman, looking confused yet pleased to see him. 'Doctor?' she said simply. 'Yes, that's me, hello' the Doctor replied. 'I'm so glad you're here,' she said, and this time it was the Doctor's turn to look confused. 'You are?' Yvonne smiled. 'Yes, there's someone here waiting for you.' The Doctor frowned. 'Who?'


	3. The Girl in the Cage

AN: OK this is it! This is when the chapters will get bigger, I promise! We also meet the new companion in this chapter, but before then I've got a little lecture. I want this story to involve the reader as much as possible, so I want you to throw at me anything you'd like me to include in the story. And I will include it, even if this story takes me years. A name for a new character, an already met character (even dead ones or ones like Donna, the TARDIS can travel in time remember!), plot lines, locations, anything. Even prompts. Tell me your favourite parts of Doctor Who, or make up something new that you think would make this story better. Also, I have decided not to update unless I get reviews, _but_ as soon as I get just one review I'll be on that laptop faster than you can say 'Where's she got to now?' (Little Doctor who quote there) NOT THAT FAST! Tee hee hee. Okay, lecture over, sorry about my little rant. Let's get on with the story.

'_I'm so glad you're here,' she said, and this time it was the Doctor's turn to look confused. 'You are?' Yvonne smiled. 'Yes, there's someone here waiting for you.' The Doctor frowned. 'Who?'_

'Come with me,' Yvonne smiled and promptly turned on her heel and walked briskly off. The Doctor followed anxiously, his thoughts overrun with questions. Who was waiting for him? A friend or a foe? Jack crossed his mind a couple of times, but his flirtatious friend wasn't even at Torchwood yet, and anyway he knew where to find the Doctor why would he come here?

They turned a corner and the Doctor found himself in a lift. He stepped inside and Yvonne pressed a button. The doors closed. After the hustle and bustle of the entrance hall, the lift was silent, eerily so. The Doctor could hear his own anxious heartbeat, his own ragged breath. Finally, the agonising wait came to an end and the lift stopped. Yvonne and the Doctor stepped out, Yvonne confident, the Doctor cautious. They had gone deep. Very deep. Just how far down they were the Doctor wasn't sure, but he could no longer hear the sound of life, cars and people any more. 'Where are we?' he thought aloud, and Yvonne's answer stunned him. 'This is where we keep the live specimens.' Live specimens? Yvonne had said someone, not something. This puzzled the Doctor even further. He began to see what she had meant, though. They were beginning to pass cages. Rusty, old cages, all different shapes and sizes. But they all had one thing in common. They were all empty.

They finally came to a door, and Yvonne entered a code into a keypad next to it. 'I'm afraid you'll have to understand, Doctor, I have other duties to attend to. I must leave you here. But anyway, I think you'll want to do this without me.' She pushed open the door, and walked back up the long corridor of cages. The Doctor hesitated, unsure of what to do next. He was considering following Yvonne to ask her what was going on, when he heard a voice calling from inside the room. 'Doctor? Did someone say Doctor? Yvonne is that you? Have you found the Doctor?' The Doctor froze. It was a child's voice. He stepped inside the room, and saw the largest cage yet. Inside was the grubbiest child he had ever seen. She must have been no more than 14 or 15, the Doctor thought. She spoke again. 'Are you the Doctor?' He couldn't speak, he was so full of rage at the people who had done this to her. He ran back and caught Yvonne just before she reached the lift. He grabbed her arm, fury in his eyes. 'Who is she? What have you done to her?' Yvonne looked at him sadly. 'It was… necessary. We could be sure she wouldn't try to escape. It's for her own protection.' The Doctor's anger didn't ease, not one bit.

'A HUMAN THOUGH? You did this to a human child who you have locked away down here without the sun, or human contact.' Yvonne sighed. 'That's just it though. She's not human.' The Doctor looks at her as if she was mad. 'Well she looks human to me'. The Doctor was incredulous. Yvonne reassured him. 'She's half human. Now go back to her, she's been waiting for you her whole life.' The Doctor couldn't agree with this, but his hatred of this woman and the sympathy he felt for that poor, defenceless child turned him around and he ran back in the direction of the girl.

She had been crying that much was clear. She looked up in hope when he entered, and her face lit up at the sight of him. He sat down on a chair in front of her cage. 'Why don't you just run away?' He said, almost in tears himself. 'It's for my own good. Now, down to business. How old are you?' The Doctor was shocked. 'What? How old am I?' 'Yes, that's just what I asked you, silly,' She giggled. 'Well, I'm older than you think I am.' He leaned in slowly. 'I am over 900 years old.' The girl didn't flinch. 'So you're, hmm let me see. Eleventh regeneration. No tenth. No… eleventh, definitely eleventh.' 'How can you possibly know that?' the Doctor asked, amusement clearly showing on his face. 'I had a good teacher.' 'So someone taught you about me?' The Doctor clearly didn't have a clue what was going on. So he decided to go back to basics.

'What's your name?' That was always a good place to start wasn't it? 'I have many names,' the girl whispered, and the Doctor had to lean in to hear her. 'My people gave me a name, but the human part of me doesn't understand it. So you must call me by my human name. Suzanne. But please call me Suzie.' 'Suzie it is then,' the Doctor smiled, glad they were getting somewhere. 'So tell me about you,' Suzie looked at him quizzically. The Doctor sighed impatiently. 'Where you come from, where your family is, how you ended up here on Earth.' Suzie smiled. 'It's a long story.' The Doctor grinned, and glanced down at the bars of the cage. 'Well, I don't think you're going anywhere for the foreseeable future, so I think we've got a while.' 'Ok then, I shall tell you my story…'


	4. The Truth

AN: First a shout out to my two new followers, marmitehaters57 and SomeRandomPerson12! A special thank you to marmitehaters57 for reviewing, so this chapter's for you!

'_So tell me about you,' Suzie looked at him quizzically. The Doctor sighed impatiently. 'Where you come from, where your family is, how you ended up here on Earth.' Suzie smiled. 'It's a long story.' The Doctor grinned, and glanced down at the bars of the cage. 'Well, I don't think you're going anywhere for the foreseeable future, so I think we've got a while.' 'Ok then, I shall tell you my story…'_

'Many years ago a great war swept through time and space. The Time War.' The Doctor opened his mouth to say something, but she held up a finger and he fell silent. She waited for a second and then continued. 'A crack opened in time and a young man from Earth fell through it. He ended up on my world. He fell in love with the planet, and in turn fell in love with a woman. She looked his age but she was so much older. He didn't want to leave, he had no life on Earth and here on this planet he had found happiness. The woman was mourning; she had lost her son to the rest of the universe, he had left without a trace. Her happiness was restored by this handsome stranger, though. In time, she gave birth to a daughter. But then the Time War raged across the universe, and the human, who had come to call his new world his home, left to fight for his new people. He was killed instantly, a weak human with no knowledge of combat. The woman was driven to despair. The war was reaching her and in a final act of desperation she pushed her daughter, who was just a child, through the crack. It closed before the woman could follow. The war ended, the planet was lost. The woman died because, many years later, a man called the Doctor closed the cracks in time and space. Many years later, the Doctor would kill her, doing something he thought was right. You are the Doctor. You killed my mother.'

There was a long pause. The Doctor just stared at her, before muttering 'the cracks were going to absorb the universe.'

'I know. But not every crack was a bad one. Some provided hope, or would have if you hadn't stopped them.'

'It was your mother who was killed.'

'Yes.'

'So you've come here from your own world years ago, and allowed yourself to be imprisoned all this time while waiting for me to open the cracks, go back in time and save your mother. Is that what you want? That is what you want isn't it? That's what you've been waiting for?'

Suzie met his gaze levelly. 'No'.

'The Doctor was stunned into silence for a few seconds. 'No?'

'No.' Suzie was smirking now. 'I miss my mother, of course I do, but no.'

'So what do you want?'

'You were right, Doctor, you were right about many things. I was pushed rough the crack leaving my mother behind. I have allowed myself to be imprisoned for many, many years whilst waiting for you. But you missed one thing, one important detail that makes all the difference. I _allowed_ myself to be imprisoned. I wasn't captured, wasn't forced in here because I was half an alien. I walked in here myself. I had been told to find you and so I knew. I knew that if you came here by accident you wouldn't just leave. You would want to find out more.'

'But if you don't want my help then why were you told to find me?'

'Do you know _why_ you came here by accident? It was me.'

'You hacked my ship's controls?' The Doctor was horrified. 'How could you do that from here?'

'I didn't hack your controls. I didn't do a thing. Your ship sensed something it hadn't sensed in a long time, and so thought you might need to see it. Just like I knew it would. I'm an anomaly, you see.' She looked almost proud. 'Only one like me in the universe. There have been others _like_ me but they aren't the same because both their parents are human. In fact you're married to her, aren't you? Congratulations, by the way. Oh, don't look so surprised. We're in Torchwood, I hear everything.'

'So you're not just any human+?'

'Nope. Human + Time Lord.'

Then there was a silence that lasted minutes. At least 10, in fact. Suzie was quite happy just to sit there and admire the Doctor's expression. He was going through all sorts of emotions. Unequally happy, unbelievably sad. Then he just looked content, like it all made sense now.

'So your mother not only saved you from the Time War…'

'…But from the destruction of Gallifrey itself. Yes,' finished Suzie. 'But I'm not done yet. There's something else I need to tell you. I told you that my mother's son had been lost to the rest of the universe, gone without a trace. He was a thief as well. He stole a ship, a type 40 TARDIS from his own people. Then he set off to see the stars. Sound familiar?'

The Doctor held up a hand, his eyes filling with tears. He had heard enough. He had just been told that effectively he had killed his own mother. Closing the crack that would have seen her to safety with her young daughter. DAUGHTER! His eyes flew open to see Suzie smiling at him.

'Hello Doctor. My half-brother. That's what I was waiting for. You. The TARDIS sensed a Time Lord and so brought you here. I'm not 14 years old, I'm 114. I've been waiting for you my whole life, so please,' she leant forward, pressing her face up against the bars, 'take me with you.'

The Doctor gave her the biggest grin he had ever given, he had never been happier in his entire life. He could never have saved his mother, he sees that now. The cracks had to be closed, she would have not only died but died without a memory and he was glad he and Suzie could still have that. So he told Suzie the only thing he wanted to say, and the only thing he could.

'Of course you can Suzie, I couldn't imagine anything better.'

Of course, in reality it proved much trickier. There was the hassle of persuading Torchwood that she would be safer with him, that he couldn't well leave her now that he knew who she was. They took a lot of persuading, but they eventually gave in, on the condition that if she was ever harmed she was the Doctor's full responsibility. And that he filled out forms. A lot of forms. Suzie had never seen so much paper in her life. Neither had the Doctor for that matter, and that was quite an achievement. After all the paperwork was finished though, they were finally allowed to leave and the first thing the Doctor did was show Suzie the TARDIS.

'It's beautiful,' she breathed. 'Just like mother said it would be.' The TARDIS hummed her approval for Suzie and for the Doctor actually following her instructions FOR ONCE.

'So,' the Doctor said, twirling around happily. 'The kitchen is to your left, your bedroom is wherever the hell the TARDIS decides to put it and this is the main control room. Any questions?'

'Yes, one.' Suzie frowned and pointed at his neck. 'What is that?'

'Why it's a bow tie, it's-'

'Cool.' Suzie nodded in approval.

The Doctor grinned. They were going to get on _very _well.

Not, however, _that_ well as it turned out. An hour later Suzie was sat stubbornly on the steps leading to the kitchen, looking bored.

'Can we go now?' she whined, sounding more like how old she looked than how old she really was.

'Yeah alright hang on in a minute have you done everything I said?'

'Yes I had the shower but the water was hot, I put on the clothes but they were itchy so the TARDIS gave me some others. These are nice.'

The Doctor walked in suspiciously. Suzie was wearing a simple purple and black stripy jumper with skinny jeans. He smiled and walked up to her, and brushed a stray blonde curl out of her face.

'You look lovely; the TARDIS did a great job.' The TARDIS hummed in agreement, almost as if to say, _see I _do_ have taste!_

'Shall we go now then?' Suzie wanted to know.

'Yes,' the Doctor said. 'Let's go.'

'York! The city that is only a city 'cos of the Cathedral, the Minster, but really it's quite a small place. It has been invaded time and time again, by the Romans, the Vikings and many many more! Once the capital of England, it now stands as a reminder to how truly great the British are, filled with landmarks and a place on the map of great historical significance. You gotta love York.'

'Great! So what's that?'

The Doctor peered into the sun, squinting at whatever Suzie was pointing at. He gasped in horror.

'That, my dear sister-'

'Half-sister,' she corrected him earning a glare from the Doctor and in turn him getting a smirk from her.

'My dear _half_-sister, that is a-'

'MONSTER, IT'S A MONSTER!'

Both Time Lords turned to see the owner of the voice, a very full-lunged and large lady shouting and pointing at what the Doctor had been about to describe.

'_That_ is something I defeated long ago and thinks I'm dead,' gulped the Doctor. '_RUN!'_

The Doctor and Suzie sprinted for their lives, away from the creature, although Suzie had no idea _why_.

'What's wrong with it?' Susie gasped breathlessly as she and the Doctor turned into a deserted alleyway and slowed to a jog. 'It wasn't harming anything, was it?'

'Not yet it isn't' the Doctor explained, 'but it can't know I'm here, or all my work will have been for nothing.'

'What do you mean 'work'?' asked Suzie.

'Oh, it's a long story and not one for right now but basically if it knows I'm alive we're in BIG trouble.'

'Why?' asked Suzie, a puzzled expression on her face.

The Doctor leaned in, gasped out 'because I'm supposed to be dead,' and then sped off in the opposite direction, leaving Suzie to try and catch up with him.

'But why are you supposed to be dead?' Suzie wanted to know.

'Because at the fields of Trenzalore, at the fall of the Eleventh, a question will be asked. A question that must never be answered. The question is 'Doctor Who?' So certain people want me dead.

'The fall of the Eleventh,' Suzie said quietly.

That stopped the Doctor in his tracks, causing Suzie to run past him. He jogged to catch up with her and then they both stopped.

'What do you mean?' the Doctor was scared now, why did that mean something to her?

'The fall of the Eleventh,' Suzie looked expectantly at the Doctor. Seeing he still didn't get it, she said in barely more than a whisper, 'you're in your eleventh incarnation.'

The Doctor stared at her for a long time. But he just couldn't think about whether she was right or not because he remembered what was in the city with them.

'Come on, we've got to go,' he yelled at Suzie, who snapped out of her trance, nodded and ran after him. They eventually came to the city walls. The Doctor realised he didn't actually know which year it was, but the walls were still intact so he guessed it was pretty far into the past. He sat with his back against the wall, breathing heavily.

'What was that we saw?' Suzie asked nervously.

The Doctor looked at her.

'A silent,' he said.


	5. How to Trap a Silent

AN: This chapter is for SomeRandomPerson12 who was so kind to follow this story. Thank you!

'_What was that we saw?' Suzie asked nervously._

_The Doctor looked at her._

'_A silent,' he said._

'A what?' The Doctor looked at Suzie.

'I'm sorry Suzie, we should never have come here I should never have brought you here.'

'Why? Is it dangerous?'

'They think I'm dead. If they know I'm alive they'll kill me, and they'll probably kill you too, in the process.'

Suzie looked horrified. 'Then let's get back to the TARDIS!'

The Doctor sighed in resignation. 'Except…'

Suzie finished his sentence in realisation. '…except the Silent is there. What're we gonna do? The silent may have moved for all we know, we could try and get back to the TARDIS.'

'No, it's far too much of a risk, we might run into it on the way, and anyway there's something else, something I'm missing…'

Suzie looked confused so the Doctor explained.

'We're really far in the past. I'm not sure when but it's certainly not somewhere I'd expect the Silence to be. A small city? In the past? It's not really their style. They're here because they followed us. They know I'm not dead.'

'Doctor, I know it sounds strange but…'

'You've forgotten what it looks like? Yeah, me too. They edit themselves out of your memory as soon as you look away. A clever tactic, but a tricky one to work with. All my instincts are telling me to run but we can't leave because the Silence can kill with electricity. All the people in this city are in danger.'

He heard a quiet and evidently scared but determined voice coming from next to him.

'So let's save them.'

It took less than 2 minutes for the Doctor to work out what to do. The plan was simple. Suzie would go looking for the silent but before it could kill her she would tell it she knew where the Doctor was. It would follow her, with her looking at it at all times, and she would lead it into the centre of the minster, where she would lock it in a room and the Doctor could talk to it. After all, there was no electricity back then so it couldn't harm them! It wasn't a great plan, with a lot of room for failure, but it was the best either of them had got and they were fast running out of time. They hugged goodbye, wished eack other good luck and set out to defeat the silence!

It was dark by the time they split up, but Suzie wasn't afraid of the dark. She had spent nearly 100 years in a cell with no windows, so this was practically normal for her. She edged her way through the quiet streets, thankful that those 100 years meant that she could see in the dark as well as she could in the light. She felt safe in the dark. It protected her. She stealthily moved through the town, and finally came to where the TARDIS was. She nearly gasped in fright when she peered around the blue box and saw that the silent hadn't moved. It was looking right at her. It was horrible now she looked at it, with a massive bulbous head and huge fingers that hung by its sides. She gulped back a scream, and found courage from someplace deep within that she didn't know she had. She stepped out from the shadows and confronted the hideous creature.

'I know two things about you. I know what you are and I know what you want. You are part of the silence, and you want the Doctor.'

'How do you know this, you are a mere human?' She winced at its harsh voice that sounded like scraping metal.

'I… heard about you. From another of your kind. I live in this city, and I want to help you. I know where the Doctor is, I'll take you to him.'

'Yes, I will come with you.'

'Really? That was easy! I mean, thank you, I understand you want this.'

She turned in the direction of the Minster, still keeping an eye on the Silent, and started walking. Thank God, she thought. It didn't see us when we arrived. It must have been facing the other way.

'You are foolish.'

The Silent interrupted her thoughts.

'R-really? Foolish? How so?'

The next two words would come to haunt Suzie because of the realisation they brought and the absolute terror that came with it.

'Your clothes.'

Suzie looked down at her jumper and jeans, so out of place against the backdrop of the past, and screamed.

'DOCTOR!'


	6. Regeneration

AN: This chapter is for AriannaSaffyreMalfoy, my darling I truly love you (but not in that way, what way?). Also, thankyou to SomeRandomPerson12 for recommending this to friends and adding it as a favourite! I am going on holiday for 2 weeks and 3 days though so no updates but I will still be able to check my emails, so I can reply to reviews! Enjoy the chapter!

'_DOCTOR!'_

The Doctor's ears pricked up at the sound of his new found sister's scream. He had only just met her, and yet already found an overwhelming urge to protect her. There was something about her that intrigued him. She was old and yet so very young at the same time. Wise and yet so innocent. When he heard her scream, however, it was a child's cry of absolute terror. She definitely sounded young now. As all his instincts kicked into action, he found himself next to the TARDIS, staring at her without really knowing how he got there. She turned and saw him, and her face lit up in hope. The Doctor melted inside. It was the way she had looked at him when he first agreed to take her with him. He should have been concentrating. If he had the Silent might have shot him, not her.

Everything seemed to go in slow motion from that point onwards. Suzie's scream of agony, her twisting and falling to the ground awkwardly, him running towards her. Suddenly he had a gun in his hand. He had forgotten that he had found one in the TARDIS and put it in his pocket just in case. That was so unlike him. Had Suzie changed him? Was he prepared to sacrifice his morals to protect her? The gun went off. He stared at it. Then at the Silent. It was dead.

He knelt beside Suzie, and cradled her in his arms. Tears sprang to his eyes.

'Doc-tor?' Suzie whispered weakly. 'Am I going to die?' The Doctor ignored her.

'Can you regenerate?' The Doctor wanted to know.

Suzie smiled weakly. 'I'm half human half Time Lord. Half my traits are human, half Time Lord. I have one heart, so I guess I can regenerate. Otherwise the human part would be dominant, and I doubt that.' Her hands began to glow. 'Yep, I definitely can. Oh, but I'm scared, Doctor, oh so scared. What do I do?'

'Sh, sh, just follow your instincts. Be magnificent.' The Doctor carried her into the TARDIS and placed her on the chair.

'I thought you said the Silent shot with electricity?'

'It does, so it must have got electricity from another time. The only thing that stops them is water.'

Suzie's eyes had closed. 'No, don't give up on me now; we've got so much more to do, you and me, eh? So much more to discover.' Suzie's eyes snapped open. She grinned.

'I know.' Then she jumped up and threw her head back, light streaming from her hands and face. The Doctor ducked behind the chair and lay on the ground, dodging the regeneration energy that would surely knock him out if it hit him. Suzie let out a cry, and then fell to the floor. The Doctor crawled over to her to see if she was alright, and she opened her eyes and smiled weakly. Then the Doctor noticed something. He sat up in confusion.

'You haven't changed!'

'I'm sorry?'

'You haven't changed. You're healed but you look the same. You _are_ the same!'

'Half human remember! That must be a human trait. Humans don't change so why should I? Plus,' she squirmed uncomfortably, 'I don't wanna shed my skin!'

The Doctor laughed.

'That's not _literally_ what we do you know!'

Suzie grinned. 'Oh, I know. I'm just teasing. And I'm just so happy to be alive!'

'Me too,' the Doctor smiled. 'So,' he clapped his hands and rubbed them together enthusiastically, 'who's for fish fingers and custard?'

'What?' Suzie pulled a face.

The Doctor looked at her in horror. 'You've _never_ had fish fingers and custard? You haven't _lived_! Come with me.' Then he grabbed her hand and whisked her off to the kitchen to try his favourite delicacy, both of them laughing and jumping all the way.

It was good to be alive.

On a spaceship far away, the Head Commander looked down at his fleet. And by calling himself the 'head' the Commander was being _very_ literal indeed.

'Er, sir?' his useless servant Jay Tee snivelled. 'We've found them.'

The Commander grinned, showing a gold tooth. 'Finally I can take my revenge on him. He thought I had died, well! He was wrong about that, wasn't he Jay? Because if there's one person who can survive _anything_, it's Max Capricorn!

AN: _DUN DUN DUNNNNNNNN!_ Let me know what you think of this chapter, and I'll update in 2 weeks and 3 days' time! Happy holidays!


	7. Max Capricorn

**Hey guys! Sooo glad to be home, but I've had a great holiday! I've missed writing, though. I'm excited about this chapter, because it introduces the main plotline XD. Also, 322 views! You guys are AWESOME! Could we have a few more reviews though, chaps? Thanks to all those who did.**

The Doctor and Suzie spent the next hour eating fish fingers and custard, Suzie mocking it, and then having a food fight. They were quite out of breath by the end, and it seemed as though they had been laughing the whole time, which was a definite possibility. They were lost in the moment, so consumed in their happiness that at first they didn't even hear the teleport in the main control room. But not for long. The Time Lord's sharp senses rarely failed them, and both looked up in confusion.

'Was that a…?' Suzie began, and then looked at her brother in horror, both knowing what the end of her sentence was. They fearfully crept through the long corridors until they reached the control room. They peered around the door, and what they saw caused Suzie to faint and the Doctor be so shocked he failed to catch her.

'Can it be…?'

Max Capricorn grinned, showing a dirty gold tooth. 'Yes Doctor. I have returned.'

Suzie came round just then and stared into the horrific face that had caused her to faint, and felt dizzy again. She leant on the Doctor for support, trying not to look at the life support the head was attached to. The Doctor put his arm round her protectively.

'How did you survive? You were pushed into the Titanic's engines!' Suzie looked shocked.

'_You_ were on the Titanic?'

'Err, not that one, long story, I'll explain later.' Suzie frowned.

'Ok. So who is this, then?'

'I'm Max Capricorn, young lady. You're very pretty, aren't you?'

Suzie shrunk into the Doctor's side and his arm around her tightened. He gave her a reassuring squeeze.

'You wouldn't dare touch her. You know who I am. I'll ask you again, how can you possibly be alive?'

'Simple, really. I had no power over it. I landed on a ledge and reprogrammed one of my angels to rescue me. They were so very loyal, in the end. Oh but, didn't you have a friend, the one that tried to kill me? What was her name? I forget these things, she wasn't important you see, a mere waitress. But no matter, the point is she failed. She died for nothing.'

Suzie could see the Doctor was consumed with fury, and she held him tighter, more to hold him back rather than to protect him. She looked up at his face. His mouth was set in a firm grimace of hatred, and his whole body was shaking, but his eyes were full of sadness and resignation.

'Her name was Astrid Peth, and she is not dead. She is very much alive.' He grew louder. 'She is travelling among the stars, just like she always dreamed.' He then sighed, and his voice shrank to no more than a whisper, causing Suzie to lean in and Max to wheel forward. 'She's happy. I think.'

Suzie could see he was about to break down, and hugged him sympathetically, as if she was holding him together. Max laughed a cruel, harsh sound that made Suzie look round at him in anger.

'I haven't come here to talk the past. I'm here about the future. See, I was on my way to seek my revenge on you, but it seems someone else has got a better idea. So I'm just gonna sit back and watch the fun. After all once was lucky, twice was a privilege, and who knows? Maybe you've been fooled in exactly the same way for a third time!'

Something about his words tugged at the Doctor's memory, from a time not so long ago before he knew Suzie. He shrugged it off, and that's when he saw Suzie. She was shaking in fear. Obviously, Max was really frightening her.

'Go into the kitchen, Suzie, and wait for me there. I'll come and find you.' Suzie nodded and ran off.

'There's two reasons she's scared, you know,' Max taunted. 'One is what I'm about to tell you, but she doesn't know that. She just knows she's in danger, somehow. The other reason is that she doesn't know why or how. It's just reality seeping through.'

Again, something about what Max was saying seemed familiar to the Doctor.

Max continued in his horrible, drawling voice. 'You see Doctor; you think you're safe, that everyone knows you're dead. But you're wrong. They know everything. And to make sure the job will be done, they've used a tactic they've used before, because they know it works. They've sent someone to keep an eye on you, but someone they can keep for themselves.' He leant forwards, and the Doctor could smell his disgusting breath, he was so close. The Doctor knew he should back away, but something about what Max was saying kept him rooted to the spot, wanting to know more. 'Your sister, she's not who you think she is. Not who _she_ thinks she is. And _that's_ why I'm here. Not to get my revenge. But to help someone else do it for me. To pass on a message, to convey a warning.'

With that, Max teleported out of the control room, leaving the Doctor standing there, shocked. He knew he should run to Suzie, what he'd just heard confirmed his worst fears; that his new found happiness was a fake. A fraud. A manipulated lie. But he couldn't move. It wasn't until he heard the splash that he leapt into action. He ran through to the kitchen, just in time to see the flesh dissolving into the ground. There was nothing left of Suzie. He sat down heavily in a chair.

'Oh Suzie, I'm so, so sorry about this,' he mumbled defeatedly.


	8. Some Old Friends

**This chapter is for Tallulahthewildgirl! Thanks so much! I am going to the Paralympics (oh yea) tomorrow for four days so no updates but I will write as soon as I can. This chapter may include some familiar faces!**

The Doctor stared at the puddle of flesh slowly dissolving into the floor that was once his sister. At first he felt anger that she had been lying to him, that she was really on their side. Then he just felt sadness, that _of course_ it wasn't her fault, she couldn't have possibly understood what was going on, he had been in the same position with Amy before. The memory of Amy's plight drove him to anger once more. Why did it always happen to _him_? Why not pick on someone else? Then he realised, and sighed in defeat. He was too _loud_. He had been too obvious, saving the universe, defeating evil. He was clever, of course he was, but he wasn't sly enough. People had started to notice, involved him in prophecies, legends. Even his name had significance in many languages. This was why he had wanted to lie low for a while, step back into the shadows. To protect himself, and those he loved. But now he had failed. He felt a surge of fear. Where was Suzie? Where was she being kept? Or, most importantly; _what was going to happen to her now?_

He leapt up from the chair, and idea hitting him. He needed help, that much was clear. But where from? The last time this happened he had called on unpaid debts and favours. So why not do the same. Within seconds he was on the phone to his favourite time agent.

'Hello Jack? Yes, it's the Doctor. Yes, I did, that's probably why I sound different. Look, I haven't got time for this now. I need your help…'

'Amelia Pond my dear, how are you? Good, and Mr Pond? Oh dear, I feared as much. Well tell him I prefer it. I thought we'd agreed. Never mind, I need you to meet me…'

'River. I need you.'

One by one, the Doctor hugged, shook hands with, and in River's (and Jack's) case, kissed his friends. He got to his oldest friend last. They shook hands, and the Doctor lingered, his gaze hovering over him.

'So,' Jack said uneasily. 'You regenerated. Properly this time.' The Doctor laughed, remembering when he had cheated death before and not changed his face. He stopped, remembering when Suzie had done the same. He swallowed back a sob. The others looked at him sympathetically. He wondered how they could know about Suzie, then realised that River probably knew from the future and had told them. He felt a surge of hope. Did that mean he would find her? Or would she just be a memory? The one person he had been in charge of protecting, and he had let her slip away. What did that make him, now?

He had only known her for a few days, but she had been waiting for him all her life.


	9. Demon's Run

**Sorry I haven't been quicker in updating, I was at a friend's last night. I go back to school tomorrow, so updates will probably be shorter and less often, but I will try to write as much as possible. I'm really enjoying the way this story is coming along.**

The Doctor's friends could see he was in a bad way, so Amy immediately started speaking to him in a really cheery way to lighten the mood. It snapped the Doctor out of his gloomy state, and he barked out instructions like an army officer to the rest of his friends. They grinned. At least he was talking now.

'River! I want you to set the co-ordinates for Demon's Run, it's worth a shot, and it's probably the same group of … people that are in charge of all this as last time.'

Amy shivered at the memory. 'But won't that be too obvious? They've already used it before?'

'Exactly. This is a trap for me, remember? They've got Suzie to get me to go there, and they'll want me to be quick about it.'

'Then we're walking into a trap. Again,' Rory sighed.

'Yeah, I know, but I can't just let them have Suzie. She's been locked away for too long.'

With a soft bump, the TARDIS materialised.

'We've landed,' River said as if it wasn't obvious. They all stepped out cautiously and peered around nervously.

'Right then you lot, let's split up, we'll cover ground faster. Ponds, you go with Jack. River, you're with me.'

'Ooh,' Jack teased. 'And Amy you're _married_? To _this_ guy? Dammit.'

'Oi, that's my wife you're talking to!' Rory grunted protectively, instinctively stepping in front of her.'

_Half an hour later_

'Ssh Jack, I think I can hear something!'

**I know it's a random place to end and it's really short, but I'm kinda busy getting ready for school.**


	10. The Doctor Worries

**Sorry I haven't updated sooner, the first two days of term are surprisingly hectic! But because today is one of those rare occasions where I have no homework, I'm gonna make this chapter longer than it would normally be. But I can't write for too long, as Waterloo Road is on tonight! Priorities, priorities! (Though if I had to choose between Doctor Who and Waterloo Road, I wouldn't hesitate in becoming a lifetime nerd and choosing Who, which I am and have already anyway.) I just gotta give this chapter to marmitehaters67, who has done nearly everything you can do to show you like a story. Also, sorry you didn't quite understand the last chapter; I hope this will make it easier for you!**

Suzie sat on the cold ground, and hugged her knees tightly to her chest. She rocked back and forth, trying to comfort herself; she felt she was on the verge of hysteria. She was so confused. Only moments ago she was with her beloved older brother, having just regenerated and now frightened for reasons she didn't quite understand, and she had gone into the kitchen. Then suddenly, everything was clear. She wondered why everything hadn't seemed blurry before, when she was with the Doctor, but maybe that was just because she had forgotten what clarity looked like. She tried to think back to when she was taken from her previous cell, the one deep underground beneath Torchwood Tower, but all she could remember was Yvonne Hartman's satisfied grin as they dragged her away. She must have enjoyed lying to the Doctor. Suzie moaned in frustration. She had been _there_. The whole time. She remembered everything that had happened, the Silent, the regeneration, Max Capricorn. Even the look in her brother's eyes when she told him who she was. All that wasn't about to be taken away from her, was it? She and the Doctor were just getting started. There was so much more to see, and do. She couldn't stop yet.

Just then, she heard the sound of hushed voices, and shuffling. She craned her neck to see what was going on, but couldn't see a thing, it was so dark. Even for her, whose eyes had become so adjusted to the dark after 100 without the sun? She murmured a shaky greeting.

'Ssh Jack, I think I heard something!'

'What is it? _Rory you're standing on my foot!_'

'Oh, er, sorry Jack.'

'Shut the _hell_ up, guys, I need to listen. _Ssh!_'

'H-hello?' A timid voice called out. 'Who's there?'

'I've found a light switch. Hang on!' The dim lights flickered into life. 'Are you Suzie?'

'Yeah, who wants to know?'

'I'm Amy Pond; this is my husband Rory and our friend Jack. I'm the Doctor's mother-in-law.'

Rory shivered. 'It still gets me every time you say that.'

'You're friends of the Doctor's?' Suzie leapt up and gripped the bars of her cage in anticipation.

'Yes, and we're here to get you out,' added Jack.

'How?' Suzie asked.

'With imagination, cunning and a sonic screwdriver. Rory and Jack run and find the Doctor, will you?'

'Why do I need a helper?' Rory whined.

'Because otherwise, you'd get lost,' Amy retorted in a sickly sweet, over the top voice.

'Oh, all right, but I'm not happy about this, though. I can cope on my own. You're gonna have to make it up to me, Amelia Pond,' Rory demanded.

'Aww, Rory, I'm not so bad, am I? We're gonna have fun, us boys, aren't we?' Jack clapped Rory on the back. Rory groaned. Amy and Suzie laughed.

'Are they always like this?' Suzie giggled.

'Actually, they just met,' Amy realised. 'But enough chit-chat, get to it lads!'

Rory and Jack ran off. A few minutes later, they were back with the Doctor, who was thrilled to see Suzie again, and that she was safe. He ran up to the doors of her cage, and with a swift motion, unlocked the doors. It was like their meeting all over again. The Doctor swept Suzie up in a tight embrace, held on to her and whispered words of comfort and relief in her ear in Gallifreyan. Then Suzie hugged Amy, Rory and Jack, thanked them for finding her, and was introduced to River. The Doctor was suddenly worried that they might be caught, so they all swiftly ran to the TARDIS. Normally the Doctor would have investigated her captors further, but he was so relieved to have his little sister back, and was so worried he would lose her again, that for the first time in his life he left it for another day. He shrugged off his anxieties, and suggested they all go to the kitchen for a celebratory dinner. Amy insisted on cooking, and the Doctor agreed on one condition: that he made his own refreshments. They all groaned when they realised what that would be, except Suzie, who was surprisingly well adjusted to the Doctor's weird eating habits, and ate fish fingers and custard just like the Doctor.

'The worst part is that it's actually kind've tasty!' Suzie exclaimed. When everyone (except the Doctor, who grinned) looked astonished, she added; 'Allons-y!' To which everyone laughed, especially the Doctor, Jack and River, who remembered his previous incarnation's catchphrase. Now it was Suzie's turn to look puzzled, having just unwittingly dredged up so many memories for the more experienced members of the TARDIS crew.

When they finally dropped off everyone except River, who the Doctor had insisted should stay the night, Suzie let out a huge yawn.

'Right, sis, that's proof more than anything that you should be getting to bed,' the Doctor smiled.

Suzie nodded. 'Alright, then. G'night!'

'Night!' The Doctor and River chorused. Suzie trudged tiredly up the TARDIS steps. The Doctor smiled at River. She grinned back.

'Alone at last,' she sighed. 'And about time too.'

She kissed the Doctor softly, and he eagerly responded to the kiss. Grinning, he led her up the TARDIS steps to the cosy living room, where the TARDIS had conveniently lit a fire. The Doctor lay on the fur rug, and River lay next to him. With her head on his chest, and one hand stroking her hair, they spent hours talking and then just staring at the ceiling, thinking. It was early in the morning when they finally fell asleep.

It wasn't entirely peaceful, though. The Doctor awoke with a start. It was dark, the fire had gone out. River was fast asleep on his chest. He stared at her beautiful face, and sighed happily. Then he frowned anxiously. He still didn't know for sure who had captured Suzie. It could have been the Silence, but he couldn't just presume. That might be walking straight into a trap. He needed to find, if he didn't want to risk losing her again. Her life could be put in danger because of him. This realisation hit him hard, and he burst into soft, silent sobs. Luckily, River didn't wake. Then another thought struck him. Max had said _someone to keep an eye on you_. Did that mean they could watch him through Suzie's eyes? If so, this was new. This hadn't happened the last time. Unless it _had_? Had the Doctor been watched the whole time Amy and Suzie were Flesh? It explained how, this time, they knew he wasn't dead. The connection was definitely broken now, of that he was certain…

But that was the _only_ thing he was certain of now.


	11. Big Mistake

**Okay guys, this is it, the final chapter! ;( But don't worry; I have already started planning the sequel, which will be my next story, and I will start it very soon! So you won't have to wait for long.**

Suzie stretched sleepily and slowly opened her eyes. The first thing she noticed was how bright it was. Or, how _not_ dark it was. Then she realised how comfortable she was. She was in a _bed_. It took her several dizzy moments to work out where she was, like when you're at a friend's and you wake up and panic, and have no idea where you are or why you're sleeping on the floor. When she eventually figured it out, she remembered what had happened, and why she recognised this room, even though technically she had never been in it, only her conscience. All these confusing thoughts were too much for her to handle first thing on a morning. This weariness brought about the realisation that she had inherited that trait from her human mother, as she guessed her Time Lord Brother was already up and about, busy as usual, though what he was doing was almost always as much of a mystery to her as to anyone else. The thought of her brother brought her leaping out of bed, and through to the kitchen. She ran in.

'Doctor! I hope you've made me a huuuge breakfast, I am practically starved…' She stopped. Usually if she wanted to find the Doctor, the TARDIS would place the room he was in right in front of her. But either the TARDIS was deliberately acting faulty, or she had gotten it wrong.

The kitchen was deserted.

The Doctor cursed himself under his breath.

'Why couldn't you leave it to another day? You _promised_ yourself you would leave it alone for a while and look after Suzie, and make sure she doesn't wander off, or explode, or—'

He stopped. He felt bad, putting it like that. This only made him more frustrated with himself.

'For all you know, she may not be _safe!_'

Suzie was bored. Like seriously, seriously bored. She had hoped the Doctor had just popped out, that he would come rushing through the door and announce he had found an adventure for them. But no such luck. It seemed she was doomed. Doomed to spend the whole day… alone. She groaned. It was more than she could bear. Suddenly, she heard crashing and cursing, and then a woman's voice laughing. She tensed, and prepared for fight or flight. Then the most eerie sound of all; the sound of silence. Suzie slowly crept to the door, and screamed at what she saw there.

The Doctor knew he wasn't far from the centre of the ship, he could hear the engines. He heard a great moan of mechanics, and then a tiny flame appearing right in the distance. Then, he heard it. An almighty boom, as if a giant had just fallen from a great height. The flame began rushing towards him. It was only 50 metres in front of him when he realised what the flame was, and cursed his perspective. The explosion raged towards him, growing ever larger and ever nearer.

It was a pity, he realised, that he was in a shaft a few metres across that stretched on uninterrupted for miles. But then again, luck wasn't exactly on his side at that precise moment.


End file.
